Tissue engineering strategies hold great potential for alveolar cleft reconstruction. Bone marrow stromal cells (BMSCs) from iliac crest and craniofacial regions are candidate seeding cells with site-specific characteristics and bone-repairing properties. Craniofacial BMSCs seem to possess stronger multipotency and osteogenic capabilities than BMSCs isolated from iliac crest. However, the angiogenic capabilities of these two type cell is rarely reported. We obtained human BMSCs (hBMSCs) of maxilla (M-hBMSCs) and iliac crest (I-hBMSCs) from same alveolar cleft patients to investigate the agiogenic variations using co-culture system with human umbilical vein endothelial cells (HUVECs). From in vitro comparison, M-hBMSCs allowed HUVECs to form more tube-like structures and sprouting angiogenesis by tube formation assays and 3D fibrin vasculogenic assay, respectively. By transplantation in vivo, M-hBMSCs enhanced larger size vessel like structures distributed the entire implants compared with I-hBMSCs. Western blotting was used to assess the angiogenesis related factors including hepatocyte growth factor (HGF), vascular endothelial growth factor (VEGF) and basic fibroblast growth factor (bFGF). The results showed a significant higher expression of bFGF protein in M-hBMSCs and HUVECs co-culture system both in vitro and in vivo. As bFGF could promote migration and proliferation of endothelial cells, scratch wound healing and transwell migration assays were performed as well as MTT assays and cell cycle analysis. The data suggested the effect of M-hBMSCs on HUVECs was stronger than I-hBMSCs. Taken together, these results indicated that craniofacial BMSCs seemed to have greater angiogenesis capability than iliac crest BMSCs and this might be associated with the different levels of bFGF protein expression in co-culture system.